Alistair Darling's future as chancellor seemed under threat today after Gordon Brown said that he had made a "mistake" in one of his parliamentary expense claims.

The prime minister was speaking after Darling agreed to repay around £700 to the parliamentary authorities having been accused by the Daily Telegraph of claiming for two properties at the same time.

In an interview this afternoon, Brown said that Darling had "apologised" for his action – even though at the time the chancellor did not appear to have issued a public apology.

Brown also repeatedly dodged questions about whether Darling would remain in his post in the forthcoming cabinet reshuffle, which some reports have suggested could come as early as Friday. Ed Balls, the children's secretary and possibly Brown's closest ministerial ally, has been tipped for the Treasury.

Today the Daily Telegraph reports that in July 2007 Darling submitted a claim for £1,004 for a service charge on his south London flat for the subsequent six-month period, during which he moved into the grace-and-favour residence of the chancellor in Downing Street.

It also said that during the six months after July 2007 he started claiming expenses relating to his grace-and-favour apartment in Downing Street, meaning that there was an overlap period when he was apparently contravening parliamentary rules saying that MPs should only claim for one second property at any one time.

Last night a spokesman for the chancellor said that the allegation that Darling had been double-claiming was "simply untrue" and this morning, in an interview on the Today programme at 8.10am, Brown said there was "no foundation" to the allegations.

"As far as I understand it, these are the same kind of suggestions that were made a few weeks ago. They've been before people who review these things and I don't think that there is substance in these allegations but obviously they have got to be investigated by the House of Commons committee that is looking at every MP including me," Brown said.

"I obviously speak to Alistair about this and he assures me that this set of allegations has no foundation in it."

But less than two hours later Darling confirmed that he would repay around £700 to cover the cost of service charge from the time he moved into Downing Street.

In a statement Darling said: "The allegation I claimed for two houses at the same time is untrue.

"I became chancellor in June 2007. In September I moved from my London flat to live in Downing Street. I made no further claims on that flat.

"In October 2007 the flat was let and the tenant moved in. The service charge was paid in advance in six-monthly intervals. When I reclaimed the cost of the service charge on July 1, I was living in the flat.

"However, because the service charge covered the period beyond September until December, I will repay the service charge from September to December."

Downing Street would not say whether Brown knew that Darling was going to repay some money when he defended the chancellor in his interview on the Today programme. At his regular briefing at 11am, the prime minister's spokesman said Darling had decided to pay back money "for the avoidance of doubt" but the spokesman would not accept the contention put to him by journalists that the chancellor had done anything wrong.

But later, in a live interview with Sky News at 2pm, Brown did criticise what Darling had done.

"I have said that what happened with Alistair was a mistake that was made. He says that it was inadvertent as a mistake and I accept that. Equally at the same time he has apologised," Brown said.

Treasury officials later said they were unaware of Darling having said any more on the matter than the statement he released in the morning – which did not contain an apology.

Brown also refused to say whether Darling would keep his job in the reshuffle. In a separate interview, for Channel 4 News at noon, Brown declined to say whether Darling would still be chancellor in 10 days' time, saying only that Darling "has been" a great chancellor.

Yesterday, before the latest allegations about Darling were published, Nick Clegg, the Liberal Democrat leader, said the chancellor ought to be sacked for profiting from his parliamentary expenses.

Clegg told BBC Radio 4's Broadcasting House yesterday morning: "He [Darling] needs to enjoy the public's trust when it comes to issues of financial probity, of money, of managing our nation's finances. And, given that very unique responsibility that he has, it's simply impossible for him to continue in that role when such very major question marks are being raised about his financial affairs."

Darling was reported by the Daily Telegraph last week to be among ministers who had paid accountants thousands of pounds of public money to complete personal tax returns, with his bills totalling £1,400 over two years. Ministers insisted the accountancy bills were in relation to their work as MPs and that the claims were allowable as parliamentary expenses.

It was also reported that Darling "flipped" the location of his second home four times in four years, allowing him to claim thousands of pounds towards the cost of his Edinburgh home and a London flat.

A spokeswoman for the chancellor said the Lib Dem criticisms were "untrue".

She said: "As Mr Darling consistently explained, he paid for personal tax advice himself. The accountant's fees claimed were for preparing his office accounts to ensure the correct amount of tax was paid. That's an allowable claim. The accountant's fees were fully declared for tax purposes and he paid tax on the benefit.

"The allegation that he changed addresses for personal gain is untrue. He changed the designation of his second home when his circumstances changed in accordance with the rules. He also pays tax on the benefit of living in Downing Street, and pays the council tax there."